diff --git a/kg_microbe/transform_utils/bacdive/bacdive.py b/kg_microbe/transform_utils/bacdive/bacdive.py index d6822d28..34d325e0 100644 --- a/kg_microbe/transform_utils/bacdive/bacdive.py +++ b/kg_microbe/transform_utils/bacdive/bacdive.py @@ -190,7 +190,6 @@ class BacDiveTransform(Transform): - """Template for how the transform class would be designed.""" def __init__( diff --git a/kg_microbe/transform_utils/bactotraits/bactotraits.py b/kg_microbe/transform_utils/bactotraits/bactotraits.py index 7aae549a..8b3608d7 100644 --- a/kg_microbe/transform_utils/bactotraits/bactotraits.py +++ b/kg_microbe/transform_utils/bactotraits/bactotraits.py @@ -38,7 +38,6 @@ class BactoTraitsTransform(Transform): - """ BactoTraits transform. diff --git a/kg_microbe/transform_utils/ctd/ctd.py b/kg_microbe/transform_utils/ctd/ctd.py index 3e745621..3dfde1d5 100644 --- a/kg_microbe/transform_utils/ctd/ctd.py +++ b/kg_microbe/transform_utils/ctd/ctd.py @@ -36,7 +36,6 @@ class CTDTransform(Transform): - """A class used to represent a transformation process for UniProt data.""" def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None): diff --git a/kg_microbe/transform_utils/disbiome/disbiome.py b/kg_microbe/transform_utils/disbiome/disbiome.py index d2d54670..773c3602 100644 --- a/kg_microbe/transform_utils/disbiome/disbiome.py +++ b/kg_microbe/transform_utils/disbiome/disbiome.py @@ -32,7 +32,6 @@ class DisbiomeTransform(Transform): - """A class used to represent a transformation process for Disbiome data.""" def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None): diff --git a/kg_microbe/transform_utils/example_transform/example_transform.py b/kg_microbe/transform_utils/example_transform/example_transform.py index 2135807c..a163149e 100644 --- a/kg_microbe/transform_utils/example_transform/example_transform.py +++ b/kg_microbe/transform_utils/example_transform/example_transform.py @@ -25,7 +25,6 @@ class YourTransform(Transform): - """Template for how the transform class would be designed.""" def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None): diff --git a/kg_microbe/transform_utils/madin_etal/madin_etal.py b/kg_microbe/transform_utils/madin_etal/madin_etal.py index 1ade4db3..425218a3 100644 --- a/kg_microbe/transform_utils/madin_etal/madin_etal.py +++ b/kg_microbe/transform_utils/madin_etal/madin_etal.py @@ -70,7 +70,6 @@ class MadinEtAlTransform(Transform): - """ Ingest Madin et al dataset (NCBI/GTDB). diff --git a/kg_microbe/transform_utils/mediadive/mediadive.py b/kg_microbe/transform_utils/mediadive/mediadive.py index deb37270..ec9318be 100644 --- a/kg_microbe/transform_utils/mediadive/mediadive.py +++ b/kg_microbe/transform_utils/mediadive/mediadive.py @@ -111,7 +111,6 @@ class MediaDiveTransform(Transform): - """Template for how the transform class would be designed.""" def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None): diff --git a/kg_microbe/transform_utils/ontologies/ontologies_transform.py b/kg_microbe/transform_utils/ontologies/ontologies_transform.py index d8ec7e8d..4ef5cdcc 100644 --- a/kg_microbe/transform_utils/ontologies/ontologies_transform.py +++ b/kg_microbe/transform_utils/ontologies/ontologies_transform.py @@ -80,7 +80,6 @@ class OntologiesTransform(Transform): - """OntologyTransform parses an Obograph JSON form of an Ontology into nodes nad edges.""" def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None): diff --git a/kg_microbe/transform_utils/rhea_mappings/rhea_mappings.py b/kg_microbe/transform_utils/rhea_mappings/rhea_mappings.py index dc984280..2c40f753 100644 --- a/kg_microbe/transform_utils/rhea_mappings/rhea_mappings.py +++ b/kg_microbe/transform_utils/rhea_mappings/rhea_mappings.py @@ -70,7 +70,6 @@ class RheaMappingsTransform(Transform): - """Template for how the transform class would be designed.""" def __init__( diff --git a/kg_microbe/transform_utils/transform.py b/kg_microbe/transform_utils/transform.py index c73dceff..4fdcd4e8 100644 --- a/kg_microbe/transform_utils/transform.py +++ b/kg_microbe/transform_utils/transform.py @@ -26,7 +26,6 @@ class Transform: - """Parent class for transforms, that sets up a lot of default file info.""" DATA_DIR = Path(__file__).parent / "data" diff --git a/kg_microbe/transform_utils/uniprot_functional_microbes/uniprot_functional_microbes.py b/kg_microbe/transform_utils/uniprot_functional_microbes/uniprot_functional_microbes.py index ea574ced..5cca7780 100644 --- a/kg_microbe/transform_utils/uniprot_functional_microbes/uniprot_functional_microbes.py +++ b/kg_microbe/transform_utils/uniprot_functional_microbes/uniprot_functional_microbes.py @@ -30,7 +30,6 @@ class UniprotFunctionalMicrobesTransform(Transform): - """A class used to represent a transformation process for UniProt data.""" def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None): diff --git a/kg_microbe/transform_utils/uniprot_human/uniprot_human.py b/kg_microbe/transform_utils/uniprot_human/uniprot_human.py index fd7aba03..f0b5fb0e 100644 --- a/kg_microbe/transform_utils/uniprot_human/uniprot_human.py +++ b/kg_microbe/transform_utils/uniprot_human/uniprot_human.py @@ -30,7 +30,6 @@ class UniprotHumanTransform(Transform): - """A class used to represent a transformation process for UniProt data.""" def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None): diff --git a/kg_microbe/transform_utils/uniprot_trembl/uniprot_trembl.py b/kg_microbe/transform_utils/uniprot_trembl/uniprot_trembl.py index 27411f32..25005b21 100644 --- a/kg_microbe/transform_utils/uniprot_trembl/uniprot_trembl.py +++ b/kg_microbe/transform_utils/uniprot_trembl/uniprot_trembl.py @@ -10,7 +10,6 @@ class UniprotTrEMBLTransform(Transform): - """Uniprot TrEMBL transform.""" def __init__( diff --git a/kg_microbe/transform_utils/wallen_etal/wallen_etal.py b/kg_microbe/transform_utils/wallen_etal/wallen_etal.py index 9609c220..06188e20 100644 --- a/kg_microbe/transform_utils/wallen_etal/wallen_etal.py +++ b/kg_microbe/transform_utils/wallen_etal/wallen_etal.py @@ -32,7 +32,6 @@ class WallenEtAlTransform(Transform): - """A class used to represent a transformation process for PdMetagenomics data.""" def __init__(self, input_dir: Optional[Path] = None, output_dir: Optional[Path] = None): diff --git a/kg_microbe/utils/pandas_utils.py b/kg_microbe/utils/pandas_utils.py index dce185dc..50e7fa34 100644 --- a/kg_microbe/utils/pandas_utils.py +++ b/kg_microbe/utils/pandas_utils.py @@ -101,7 +101,7 @@ def establish_transitive_relationship( # list_of_dfs_to_append.append(transitive_relations_df) # Create a dictionary to map objects to subjects object_to_subject = dict( - zip(subject_intermediate_df["object"], subject_intermediate_df["subject"], strict=False) + zip(subject_intermediate_df["object"], subject_intermediate_df["subject"]) ) # Filter the DataFrame to include only rows where the SUBJECT_COLUMN matches any object in the mapping diff --git a/tests/demo_test.py b/tests/demo_test.py index e8780d1d..c6b6de4e 100644 --- a/tests/demo_test.py +++ b/tests/demo_test.py @@ -6,7 +6,6 @@ class TestVersion(unittest.TestCase): - """Test version.""" def test_version_type(self):